GP-4640 add support for symlinks in fs browser, reorg actions

Ghidra/Features/Base/data/ExtensionPoint.manifest

@@ -21,3 +21,4 @@ ChecksumAlgorithm
 OverviewColorService
 DWARFFunctionFixup
 ElfInfoProducer
+FSBFileHandler

Ghidra/Features/Base/data/base.file.extensions.icons.theme.properties

@@ -38,5 +38,6 @@ icon.fsbrowser.file.extension.zip        = images/oxygen/16x16/application-x-bzi
 icon.fsbrowser.file.substring.release.   = images/famfamfam_silk_icons_v013/bullet_purple.png
 
 icon.fsbrowser.file.overlay.imported 	 		= EMPTY_ICON{images/checkmark_green.gif[size(8,8)][move(8,8)]}       // lower right quadrant
-icon.fsbrowser.file.overlay.filesystem   		= EMPTY_ICON{images/ledgreen.png[size(8,8)][move(0,8)]} // lower left quadrant
-icon.fsbrowser.file.overlay.missing.password	= EMPTY_ICON{images/lock.png[size(8,8)][move(8,0)]}				     // upper right quadrant
+icon.fsbrowser.file.overlay.filesystem   		= EMPTY_ICON{images/ledgreen.png[size(8,8)][move(0,8)]}              // lower left quadrant
+icon.fsbrowser.file.overlay.link				= EMPTY_ICON{icon.content.handler.link[move(0,8)]}                   // lower-left quadrant
+icon.fsbrowser.file.overlay.missing.password	= EMPTY_ICON{images/lock.png[size(8,8)][move(8,0)]}				     // upper right quadrant

Ghidra/Features/Base/src/main/java/ghidra/app/util/opinion/AbstractProgramLoader.java

@@ -28,7 +28,6 @@
 import ghidra.formats.gfilesystem.FSRL;
 import ghidra.framework.model.*;
 import ghidra.framework.store.LockException;
-import ghidra.plugin.importer.ProgramMappingService;
 import ghidra.program.database.ProgramDB;
 import ghidra.program.database.function.OverlappingFunctionException;
 import ghidra.program.model.address.*;
@@ -367,8 +366,7 @@ public static void setProgramProperties(Program prog, ByteProvider provider,
 			if (fsrl.getMD5() == null) {
 				fsrl = fsrl.withMD5(md5);
 			}
-			prog.getOptions(Program.PROGRAM_INFO)
-				.setString(ProgramMappingService.PROGRAM_SOURCE_FSRL, fsrl.toString());
+			FSRL.writeToProgramInfo(prog, fsrl);
 		}
 		prog.setExecutableMD5(md5);
 		String sha256 = computeBinarySHA256(provider);

Ghidra/Features/Base/src/main/java/ghidra/formats/gfilesystem/AbstractFileSystem.java

@@ -15,6 +15,7 @@
  */
 package ghidra.formats.gfilesystem;
 
+import java.io.IOException;
 import java.util.Comparator;
 import java.util.List;
 
@@ -65,6 +66,11 @@ public GFile lookup(String path) {
 		return fsIndex.lookup(null, path, getFilenameComparator());
 	}
 
+	@Override
+	public GFile getRootDir() {
+		return fsIndex.getRootDir();
+	}
+
 	@Override
 	public List<GFile> getListing(GFile directory) {
 		return fsIndex.getListing(directory);
@@ -75,4 +81,9 @@ public int getFileCount() {
 		return fsIndex.getFileCount();
 	}
 
+	@Override
+	public GFile resolveSymlinks(GFile file) throws IOException {
+		return fsIndex.resolveSymlinks(file);
+	}
+
 }

Ghidra/Features/Base/src/main/java/ghidra/formats/gfilesystem/FSRL.java

@@ -19,7 +19,6 @@
 import java.net.MalformedURLException;
 import java.util.*;
 
-import ghidra.plugin.importer.ProgramMappingService;
 import ghidra.program.model.listing.Program;
 import ghidra.util.SystemUtilities;
 
@@ -64,6 +63,7 @@
  */
 public class FSRL {
 	public static final String PARAM_MD5 = "MD5";
+	public static final String FSRL_OPTION_NAME = "FSRL";
 
 	/**
 	 * Returns the {@link FSRL} stored in a {@link Program}'s properties, or null if not present
@@ -73,8 +73,7 @@ public class FSRL {
 	 * @return {@link FSRL} from program's properties, or null if not present or invalid
 	 */
 	public static FSRL fromProgram(Program program) {
-		String fsrlStr = program.getOptions(Program.PROGRAM_INFO)
-				.getString(ProgramMappingService.PROGRAM_SOURCE_FSRL, null);
+		String fsrlStr = program.getOptions(Program.PROGRAM_INFO).getString(FSRL_OPTION_NAME, null);
 		if (fsrlStr != null) {
 			try {
 				return FSRL.fromString(fsrlStr);
@@ -86,6 +85,16 @@ public static FSRL fromProgram(Program program) {
 		return null;
 	}
 
+	/**
+	 * Writes a FSRL value to a {@link Program}'s properties.
+	 * 
+	 * @param program {@link Program}
+	 * @param fsrl {@link FSRL} to write
+	 */
+	public static void writeToProgramInfo(Program program, FSRL fsrl) {
+		program.getOptions(Program.PROGRAM_INFO).setString(FSRL_OPTION_NAME, fsrl.toString());
+	}
+
 	/**
 	 * Creates a {@link FSRL} from a raw string.  The parent portions of the FSRL
 	 * are not intern()'d so will not be shared with other FSRL instances.

Ghidra/Features/Base/src/main/java/ghidra/formats/gfilesystem/FSUtilities.java

@@ -20,6 +20,8 @@
 import java.net.MalformedURLException;
 import java.net.URLEncoder;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.text.SimpleDateFormat;
@@ -31,6 +33,7 @@
 import docking.widgets.OptionDialog;
 import ghidra.app.util.bin.ByteProvider;
 import ghidra.formats.gfilesystem.annotations.FileSystemInfo;
+import ghidra.formats.gfilesystem.fileinfo.FileType;
 import ghidra.util.*;
 import ghidra.util.exception.CancelledException;
 import ghidra.util.exception.CryptoException;
@@ -400,9 +403,7 @@ public static List<String> getLines(ByteProvider byteProvider) throws IOExceptio
 	public static String getFileMD5(File f, TaskMonitor monitor)
 			throws IOException, CancelledException {
 		try (FileInputStream fis = new FileInputStream(f)) {
-			monitor.initialize(f.length());
-			monitor.setMessage("Hashing file: " + f.getName());
-			return getMD5(fis, monitor);
+			return getMD5(fis, f.getName(), f.length(), monitor);
 		}
 	}
 
@@ -418,31 +419,47 @@ public static String getFileMD5(File f, TaskMonitor monitor)
 	public static String getMD5(ByteProvider provider, TaskMonitor monitor)
 			throws IOException, CancelledException {
 		try (InputStream is = provider.getInputStream(0)) {
-			monitor.initialize(provider.length());
-			monitor.setMessage("Hashing file: " + provider.getName());
-			return getMD5(is, monitor);
+			return getMD5(is, provider.getName(), provider.length(), monitor);
 		}
 	}
 
 	/**
 	 * Calculate the hash of an {@link InputStream}.
 	 * 
 	 * @param is {@link InputStream}
+	 * @param name of the inputstream
+	 * @param expectedLength the length of the inputstream
 	 * @param monitor {@link TaskMonitor} to update
 	 * @return md5 as a hex encoded string, never null
 	 * @throws IOException if error
 	 * @throws CancelledException if cancelled
 	 */
-	public static String getMD5(InputStream is, TaskMonitor monitor)
-			throws IOException, CancelledException {
+	public static String getMD5(InputStream is, String name, long expectedLength,
+			TaskMonitor monitor) throws IOException, CancelledException {
 		try {
+			long startms = System.currentTimeMillis();
+			long prevElapsed = startms;
+
+			monitor.initialize(expectedLength, "Hashing %s".formatted(name));
+
 			MessageDigest messageDigest = MessageDigest.getInstance(HashUtilities.MD5_ALGORITHM);
-			byte[] buf = new byte[16 * 1024];
+			int bufSize = (int) Math.max(1024, Math.min(expectedLength, 1024 * 1024));
+			byte[] buf = new byte[bufSize];
 			int bytesRead;
+			long totalBytesRead = 0;
 			while ((bytesRead = is.read(buf)) >= 0) {
 				messageDigest.update(buf, 0, bytesRead);
-				monitor.incrementProgress(bytesRead);
-				monitor.checkCancelled();
+				totalBytesRead += bytesRead;
+				monitor.increment(bytesRead);
+
+				long now = System.currentTimeMillis();
+				if (now - prevElapsed > 5000 /*5 seconds*/ && totalBytesRead > bufSize) {
+					prevElapsed = now;
+					long elapsed = now - startms;
+					long rate = (long) (totalBytesRead / (elapsed / 1000f));
+					monitor.setMessage(
+						"Hashing %s %s/s".formatted(name, FileUtilities.formatLength(rate)));
+				}
 			}
 			return NumericUtilities.convertBytesToString(messageDigest.digest());
 		}
@@ -587,4 +604,50 @@ public static void uncheckedClose(Closeable c, String msg) {
 				e);
 		}
 	}
+
+	public static boolean isSymlink(File f) {
+		try {
+			return f != null && Files.isSymbolicLink(f.toPath());
+		}
+		catch (IllegalArgumentException e) {
+			return false;
+		}
+	}
+
+	/**
+	 * Returns the destination of a symlink, or null if not a symlink or other error
+	 * 
+	 * @param f {@link File} that is a symlink
+	 * @return destination path string of the symlink, or null if not symlink
+	 */
+	public static String readSymlink(File f) {
+		try {
+			Path symlink = Files.readSymbolicLink(f.toPath());
+			return symlink.toString();
+		}
+		catch (Throwable th) {
+			// ignore and return null
+		}
+		return null;
+	}
+
+	public static FileType getFileType(File f) {
+		try {
+			Path p = f.toPath();
+			if (Files.isSymbolicLink(p)) {
+				return FileType.SYMBOLIC_LINK;
+			}
+			if (Files.isDirectory(p)) {
+				return FileType.DIRECTORY;
+			}
+			if (Files.isRegularFile(p)) {
+				return FileType.FILE;
+			}
+		}
+		catch (IllegalArgumentException e) {
+			// fall thru
+		}
+		return FileType.UNKNOWN;
+	}
+
 }

Ghidra/Features/Base/src/main/java/ghidra/formats/gfilesystem/GFile.java

@@ -31,61 +31,57 @@ public interface GFile {
 	 * The {@link GFileSystem} that owns this file.
 	 * @return {@link GFileSystem} that owns this file.
 	 */
-	public GFileSystem getFilesystem();
+	GFileSystem getFilesystem();
 
 	/**
 	 * The {@link FSRL} of this file.
 	 *
 	 * @return {@link FSRL} of this file.
 	 */
-	public FSRL getFSRL();
+	FSRL getFSRL();
 
 	/**
 	 * The parent directory of this file.
 	 *
 	 * @return parent {@link GFile} directory of this file.
 	 */
-	public GFile getParentFile();
+	GFile getParentFile();
 
 	/**
 	 * The path and filename of this file, relative to its owning filesystem.
 	 *
 	 * @return path and filename of this file, relative to its owning filesystem.
 	 */
-	public String getPath();
+	String getPath();
 
 	/**
 	 * The name of this file.
 	 *
 	 * @return name of this file.
 	 */
-	public String getName();
+	String getName();
 
 	/**
 	 * Returns true if this is a directory.
 	 * <p>
 	 * @return boolean true if this file is a directory, false otherwise.
 	 */
-	public boolean isDirectory();
+	boolean isDirectory();
 
 	/**
 	 * Returns the length of this file, or -1 if not known.
 	 *
 	 * @return number of bytes in this file.
 	 */
-	public long getLength();
-
-	default public long getLastModified() {
-		return -1;
-	}
+	long getLength();
 
 	/**
 	 * Returns a listing of files in this sub-directory.
 	 * <p>
 	 * @return {@link List} of {@link GFile} instances.
 	 * @throws IOException if not a directory or error when accessing files.
 	 */
-	default public List<GFile> getListing() throws IOException {
+	default List<GFile> getListing() throws IOException {
 		return getFilesystem().getListing(this);
 	}
 

Ghidra/Features/Base/src/main/java/ghidra/formats/gfilesystem/GFileLocal.java

@@ -16,6 +16,7 @@
 package ghidra.formats.gfilesystem;
 
 import java.io.File;
+import java.util.Objects;
 
 /**
  * {@link GFile} implementation that refers to a real java.io.File on the local
@@ -85,11 +86,6 @@ public long getLength() {
 		return f.length();
 	}
 
-	@Override
-	public long getLastModified() {
-		return f.lastModified();
-	}
-
 	public File getLocalFile() {
 		return f;
 	}
@@ -99,4 +95,23 @@ public String toString() {
 		return "Local " + f.toString() + " with path " + path;
 	}
 
+	@Override
+	public int hashCode() {
+		return Objects.hash(f, fs, fsrl, parent, path);
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj) {
+			return true;
+		}
+		if (!(obj instanceof GFileLocal)) {
+			return false;
+		}
+		GFileLocal other = (GFileLocal) obj;
+		return Objects.equals(f, other.f) && Objects.equals(fs, other.fs) &&
+			Objects.equals(fsrl, other.fsrl) && Objects.equals(parent, other.parent) &&
+			Objects.equals(path, other.path);
+	}
+
 }